4B6G

The Crystal Structure of the Neisserial Esterase D.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A glutathione-dependent detoxification system is required for formaldehyde resistance and optimal survival of Neisseria meningitidis in biofilms.

Chen, N.H.Counago, R.M.Djoko, K.Y.Jennings, M.P.Apicella, M.A.Kobe, B.McEwan, A.G.

(2013) Antioxid Redox Signal 18: 743-755

  • DOI: https://doi.org/10.1089/ars.2012.4749
  • Primary Citation of Related Structures:  
    4B6G

  • PubMed Abstract: 

    The glutathione-dependent AdhC-EstD formaldehyde detoxification system is found in eukaryotes and prokaryotes. It is established that it confers protection against formaldehyde that is produced from environmental sources or methanol metabolism. Thus, its presence in the human host-adapted bacterial pathogen Neisseria meningitidis is intriguing. This work defined the biological function of this system in the meningococcus using phenotypic analyses of mutants linked to biochemical and structural characterization of purified enzymes. We demonstrated that mutants in the adhC and/or estD were sensitive to killing by formaldehyde. Inactivation of adhC and/or estD also led to a loss of viability in biofilm communities, even in the absence of exogenous formaldehyde. Detailed biochemical and structural analyses of the esterase component demonstrated that S-formylglutathione was the only biologically relevant substrate for EstD. We further showed that an absolutely conserved cysteine residue was covalently modified by S-glutathionylation. This leads to inactivation of EstD. The results provide several conceptual innovations. They provide a new insight into formaldehyde detoxification in bacteria that do not generate formaldehyde during the catabolism of methanol. Our results also indicate that the conserved cysteine, found in all EstD enzymes from humans to microbes, is a site of enzyme regulation, probably via S-glutathionylation. The adhc-estD system protects against formaldehyde produced during endogenous metabolism.


  • Organizational Affiliation

    Australian Centre for Infectious Disease Research, School of Chemistry and Molecular Biosciences, Faculty of Science, The University of Queensland, St. Lucia, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE ESTERASE
A, B
283Neisseria meningitidis MC58Mutation(s): 0 
EC: 3.1.2.12
UniProt
Find proteins for Q9JZ43 (Neisseria meningitidis serogroup B (strain MC58))
Explore Q9JZ43 
Go to UniProtKB:  Q9JZ43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9JZ43
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.143 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.268α = 90
b = 111.268β = 90
c = 169.861γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-02-13
    Changes: Database references
  • Version 1.2: 2018-03-28
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description